The present invention relates to the synthesis of oligosaccharides. In particular, it relates to improved methods for purifying oligosaccharides using ultrafiltration, nanofiltration and/or reverse osmosis.
Increased understanding of the role of carbohydrates as recognition elements on the surface of cells has led to increased interest in the production of carbohydrate molecules of defined structure. For instance, compounds comprising the oligosaccharide moiety, sialyl lactose, have been of interest as neutralizers for enterotoxins from bacteria such as Vibrio cholerae, Escherichia coli, and Salmonella (see, e.g., U.S. Pat. No. 5,330,975). Sialyl lactose has also been investigated for the treatment of arthritis and related autoimmune diseases. In particular, sialyl lactose is thought to inhibit or disrupt the degree of occupancy of the Fc carbohydrate binding site on IgG, and thus prevent the formation of immune complexes (see, U.S. Pat. 5,164,374). Recently, sialyl-xcex1(2,3)galactosides, sialyl lactose and sialyl lactosamine have been proposed for the treatment of ulcers, and Phase I clinical trials have begun for the use of the former compound in this capacity. See, Balkonen et al., FEMS Immunology and Medical Microbiology 7:29 (1993) and Bio World Today, p. 5, Apr. 4, 1995. As another example, compounds comprising the sialyl Lewis ligands, sialyl Lewisx and sialyl Lewisa are present in leukocyte and non-leukocyte cell lines that bind to receptors such as the ELAM-1 and GMP 140 receptors. Polley et al., Proc. Natl. Acad. Sci., USA, 88:6224 (1991) and Phillips et al., Science, 250:1130 (1990), see, also, U.S. Ser. No. 08/063,181.
Because of interest in making desired carbohydrate structures, glycosyltransferases and their role in enzyme-catalyzed synthesis of carbohydrates are presently being extensively studied. The use of glycosyltransferases for enzymatic synthesis of carbohydrate offers advantages over chemical methods due to the virtually complete stereoselectivity and linkage specificity offered by the enzymes (Ito et al., Pure Appl. Chem., 65:753 (1993) U.S. Pat. Nos. 5,352,670, and 5,374,541). Consequently, glycosyltransferases are increasingly used as enzymatic catalysts in synthesis of a number of carbohydrates used for therapeutic and other purposes.
Carbohydrate compounds produced by enzymatic synthesis or by other methods are often obtained in the form of complex mixtures that include not only the desired compound but also contaminants such as unreacted sugars, salts, pyruvate, phosphate, PEP, nucleosides, nucleotides, and proteins, among others. The presence of these contaminants is undesirable for many applications for which the carbohydrate compounds are useful. Previously used methods for purifying oligosaccharides, such as chromatography, i.e., ion exchange and size exclusion chromatography, have several disadvantages. For example, chromatographic purification methods are not amenable to large-scale purifications, thus precluding their use for commercial production of saccharides. Moreover, chromatographic purification methods are expensive. Therefore, a need exists for purification methods that are faster, more efficient, and less expensive than previously used methods. The present invention fulfills this and other needs.
A method for using a combination of membranes to remove undesirable impurities from a sugar-containing solution, especially molasses-forming ions which inhibit sugar crystallization is described in U.S. Pat. No. 5,454,952. The method, which involves ultrafiltration followed by nanofiltration, is described as being useful for improving the recovery of crystalline sugar from sugar cane or sugar beet solutions.
U.S. Pat. No. 5,403,604 describes the removal of fruit juice sugars from fruit juice by nanofiltration to obtain a retentate having a high level of sugars and a permeate having a lower level of sugars.
U.S. Pat. No. 5,254,174 describes the use of chromatography and/or nanofiltration to purify inulide compounds of formula GFn (where G is glucose and F is fructose) by removing salts and glucose, fructose, and sucrose from a juice or syrup containing the inulide compounds.
U.S. Pat. No. 4,956,458 describes the use of reverse osmosis to remove from polydextrose, which is a randomly cross-linked glucan polymer produced trough the acid-catalyzed condensation of glucose, most of the off-flavor constituents such as anhydroglucose and furaldehyde derivatives polydextrose.
U.S. Pat. No. 4,806,244 describes the use of a combined membrane and sorption system in which sulfate is removed from water by nanofiltration, after which the nitrate, which passed through the membrane, was removed from the permeate by absorption to an ion exchange resin.
The present invention provides methods of purifying a carbohydrate compound from a feed solution containing a contaminant. The methods involve contacting the feed solution with a nanofiltration or reverse osmosis membrane under conditions such that the membrane retains the desired carbohydrate compound while a majority of the contaminant passes through the membrane. The invention provides methods for purifying carbohydrate compounds such as sialyl lactosides, sialic acid, lacto-N-neotetraose (LNnT) and GlcNAcxcex21,3Galxcex21,4Glc (LNT-2), NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924)(Fucxcex11xe2x86x923)Glc(R1) xcex21-OR2, wherein R1 is OH or NAc; R2 is a hydrogen, an alkoxy, a saccharide, an oligosaccharide or an aglycon group having at least one carbon atom; and Galxcex1(1xe2x86x923)Galxcex2(1xcex944)Glc(R1) xcex2Oxe2x80x94R3, wherein R1 is OH or NAc; R3 is xe2x80x94(CH2)nxe2x80x94COX, with X=OH, OR4, xe2x80x94NHNH2, R4 being a hydrogen, a saccharide, an oligosaccharide or an aglycon group having at least one carbon atom, and n=an integer from 2 to 18.
Also provided are methods for purifying carbohydrate compounds having a formula NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924)GlcN(R1)xcex2xe2x80x94OR2, NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924)GlcN(R1)xcex2(1xe2x86x923)Galxcex2xe2x80x94OR2, NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924) (Fucxcex11xe2x86x923)GlcN(R1)xcex2xe2x80x94OR2, or NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924) (Fucxcex11xe2x86x923)GlcN(R1)xcex2(1xe2x86x923)Galxcex2xe2x80x94OR2, wherein R1 is alkyl or acyl from 1-18 carbons, 5,6,7,8-tetrahydro-2-naphthamido; benzamido; 2-naphthamido; 4-aminobenzamido; or 4-nitrobenzamido, and R2 is a hydrogen, a saccharide, an oligosaccharide or an aglycon group having at least one carbon atom.
In another embodiment, the invention provides methods of purifying a carbohydrate compound from a feed solution comprising a reaction mixture used to synthesize the carbohydrate compound. The synthesis can be enzymatic or chemical, or a combination thereof. The methods involve removing any proteins present in the feed solution by contacting the feed solution with an ultrafiltration membrane so that proteins are retained the membrane while the carbohydrate compound passes through the membrane as a permeate. The permeate from the ultrafiltration step is then contacted with a nanofiltration or reverse osmosis membrane under conditions such that the nanofiltration or reverse osmosis membrane retains the carbohydrate compound while a majority of an undesired contaminant passes through the membrane.
Another embodiment of the invention provides methods for purifying nucleotides, nucleosides, and nucleotide sugars by contacting a feed solution containing the nucleotide or related compound with a nanofiltration or reverse osmosis membrane under conditions such that the membrane retains the nucleotide or related compound while a majority of the contaminant passes through the membrane.
The present invention also provides methods for removing one or more contaminants from a solution that contains a carbohydrate of interest. The methods involve contacting the solution with a first side of a semipermeable membrane having rejection coefficients so as to retain the carbohydrate while allowing the contaminant to pass through the membrane. The membrane is selected from the group consisting of an ultrafiltration membrane, a nanofiltration membrane, and a reverse osmosis membrane, depending on the size and charge of the carbohydrate of interest relative to those of the contaminants. The membrane separates a feed solution containing a carbohydrate into a retentate portion and a permeate portion. If the rejection coefficient of the membrane is greater for the carbohydrate than for the contaminant, the retentate portion will have a lower concentration of the contaminant relative to the contaminant concentration in the feed solution, and generally also a higher ratio of the carbohydrate to the undesired contaminant. Conversely, a membrane having a rejection coefficient for the carbohydrate that is lesser than that for the contaminant will effect a separation wherein the concentration of the contaminant is lower in the permeate than in the feed solution, and the permeate will have a higher ratio of carbohydrate to contaminant than the feed solution. If desired, the fraction containing the carbohydrate can be recycled through the membrane system for further purification.
Examples of contaminants that can be removed from solutions containing the compound of interest using the methods of the invention include, but are not limited to, unreacted sugars, inorganic ions, pyruvate, phosphate, phosphoenolpyruvate, and proteins.
Definitions
The following abbreviations are used herein:
The term xe2x80x9ccarbohydratexe2x80x9d encompasses chemical compounds having the general formula (CH2O)n, and includes monosaccharides, disaccharides, oligosaccharides, and polysaccharides. The term xe2x80x9coligo,xe2x80x9d as used herein, refers to a polymeric molecule consisting of 2 to approximately 10 residues, for example, amino acids (oligopeptide), monosaccharides (oligosaccharide), and nucleic acids (oligonucleotide). The term xe2x80x9cpolyxe2x80x9d refers to a polymeric molecule comprising greater than about 10 residues.
Oligosaccharides are considered to have a reducing end and a non-reducing end, whether or not the saccharide at the reducing end is in fact a reducing sugar. In accordance with accepted nomenclature, oligosaccharides are depicted herein with the non-reducing end on the left and the reducing end on the right.
All oligosaccharides described herein are described with the name or abbreviation for the non-reducing saccharide (e.g., Gal), followed by the configuration of the glycosidic bond (xcex1 or xcex2), the ring bond, the ring position of the reducing saccharide involved in the bond, and then the name or abbreviation of the reducing saccharide (e.g., GlcNAc). The linkage between two sugars may be expressed, for example, as 2,3, 2xe2x86x923, or (2,3).
A compound is xe2x80x9csubstantially purifiedxe2x80x9d from an undesired component in a solution if the concentration of the undesired component after purification is no greater than about 40% of the concentration of the component prior to purification. Preferably, the post-purification concentration of the undesired component will be less than about 20% by weight, and more preferably less than about 10%, of the pre-purification concentration.
The term xe2x80x9cpharmaceutically pure,xe2x80x9d as used herein, refers to a compound that is sufficiently purified from undesired contaminants that the compound is suitable for administration as a pharmaceutical agent. Preferably, the compound is purified such that the undesired contaminant is present after purification in an amount that is about 5% by weight or less of the pre-purification concentration of the contaminant in the feed solution. More preferably, the post-purification concentration of the contaminant is about 1% or less of the pre-purification contaminant concentration, and most preferably about 0.5% or less of the pre-purification concentration of contaminant.
A xe2x80x9cfeed solutionxe2x80x9d refers to any solution that contains a compound to be purified. For example, a reaction mixture used to synthesize an oligosaccharide can be used as a feed solution from which the desired reaction product is purified using the methods of the invention.
The present invention provides methods for rapidly and efficiently purifying specific carbohydrate and oligosaccharide structures to a high degree of purity using semipermeable membranes such as reverse osmosis and/or nanofiltration membranes. The methods are particularly useful for separating desired oligosaccharide compounds from reactants and other contaminants that remain in a reaction mixture after synthesis or breakdown of the oligosaccharides. For example, the invention provides methods for separating oligosaccharides from enzymes and/or other components of reaction mixtures used for enzymatic synthesis or enzymatic degradation of oligosaccharides, nucleotide sugars, glycolipids, liposaccharides, nucleotides, nucleosides, and other saccharide-containing compounds. Also provided are methods for removing salts, sugars and other components from feed solutions using ultrafiltration, nanofiltration or reverse osmosis. Using these techniques, the saccharides (e.g., sialyl lactose, SLex, and many others) can be produced at up to essentially 100% purity. Moreover, the purification methods of the invention are more efficient, rapid, and amenable to large-scale purifications than previously known carbohydrate purification methods.
Often, a desired purification can be effected in a single step; additional purification steps such as crystallization and the like are generally not required. Accordingly, the invention provides single-step methods for purifying saccharide-containing compounds.
To purify saccharides according to the invention, a membrane is selected that is appropriate for separating the desired carbohydrate from the undesired components of the solution from which the carbohydrate is to be purified. The goal in selecting a membrane is to optimize for a particular application the molecular weight cutoff (MWCO), membrane composition, permeability, and rejection characteristics, that is, the membrane""s total capacity to retain specific molecules while allowing salts and other, generally smaller or opposite charged molecules, to pass through. The percent retention of a component i (Ri) is given by the formula Ri=(1xe2x88x92Cip/Cir)xc3x97100%, wherein Cip is the concentration of component i in the permeate and Cir is the concentration of component i in the retentate, both expressed in weight percent. The percent retention of a component is also called the retention characteristic or the membrane rejection coefficient.
For effective separation, a membrane is chosen that has a high rejection ratio for the saccharide of interest relative to the rejection ratio for compounds from which separation is desired. If a membrane has a high rejection ratio for a first compound relative to a second compound, the concentration of the first compound in the permeate solution which passes through the membrane is decreased relative to that of the second compound. Conversely, the concentration of the first compound increases relative to the concentration of the second compound in the retentate. If a membrane does not reject a compound, the concentration of the compound in both the permeate and the reject portions will remain essentially the same as in the feed solution. It is also possible for a membrane to have a negative rejection rate for a compound if the compound""s concentration in the permeate becomes greater than the compound""s concentration in the feed solution. A general review of membrane technology is found in xe2x80x9cMembranes and Membrane Separation Processes,xe2x80x9d in Ullmann""s Encyclopedia of Industrial Chemistry (VCH, 1990); see also, Noble and Stern, Membrane Separations Technology: Principles and Applications (Elsevier, 1995).
As a starting point, one will generally choose a membrane having a molecular weight cut-off (MWCO, which is often related to membrane pore size) that is expected to retain the desired compounds while allowing an undesired compound present in the feed stream to pass through the membrane. The desired MWCO is generally less than the molecular weight of the compound being purified, and is typically greater than the molecular weight of the undesired contaminant that is to be removed from the solution containing the compound being purified. For example, to purify a compound having a molecular weight of 200 Da, one would choose a membrane that has a MWCO of less than about 200 Da. A membrane with a MWCO of 100 Da, for example, would also be a suitable candidate. The membranes that find use in the present invention are classified in part on the basis of their MWCO as ultrafiltration (UF) membranes, nanofiltration (NF) membranes, or reverse osmosis (RO) membranes, depending on the desired separation. For purposes of this invention, UF, NF, and RO membranes are classified as defined in the Pure Water Handbook, Osmonics, Inc. (Minnetonka Minn.). RO membranes typically have a nominal MWCO of less than about 200 Da and reject most ions, NF membranes generally have a nominal MWCO of between about 150 Da and about 5 kDa, and UF membranes generally have a nominal MWCO of between about 1 kDa and about 300 kDa (these MWCO ranges assume a saccharide-like molecule).
A second parameter that is considered in choosing an appropriate membrane for a particular separation is the polymer type of the membrane. The membranes used in each zone are made of conventional membrane material whether inorganic, organic, or mixed inorganic and organic. Typical inorganic materials include glasses, ceramics, cermets, metals and the like. Ceramic membranes, which are preferred for the UF zone, may be made, for example, as described in U.S. Pat. Nos. 4,692,354 to Asaeda et al, 4,562,021 to Alary et al., and others. The organic materials which are preferred for the NF and RO zones, are typically polymers, whether isotropic, or anisotropic with a thin layer or xe2x80x9cskinxe2x80x9d on either the bore side or the shell side of the fibers. Preferred materials for fibers are polyamides, polybenzamides, polysulfones (including sulfonated polysulfone and sulfonated polyether sulfone, among others), polystyrenes, including styrene-containing copolymers such as acrylo-nitrile-styrene, butadiene-styrene and styrene-vinylbenzylhalide copolymers, polycarbonates, cellulosic polymers including cellulose acetate, polypropylene, poly(vinyl chloride), poly(ethylene terephthalate), polyvinyl alcohol, fluorocarbons, and the like, such as those disclosed in U.S. Pat. Nos. 4,230,463, 4,806,244, and 4,259,183. The NF and RO membranes often consist of a porous support substrate in addition to the polymeric discrimination layer.
Of particular importance in selecting a suitable membrane composition is the membrane surface charge. Within the required MWCO range, a membrane is selected that has a surface charge that is appropriate for the ionic charge of the carbohydrate and that of the contaminants. While MWCO for a particular membrane is generally invariable, changing the pH of the feed solution can affect separation properties of a membrane by altering the membrane surface charge. For example, a membrane that has a net negative surface charge at neutral pH can be adjusted to have a net neutral charge simply by lowering the pH of the solution. An additional effect of adjusting solution pH is to modulate the ionic charge on the contaminants and on the carbohydrate of interest. Therefore, by choosing a suitable membrane polymer type and pH, one can obtain a system in which both the contaminant and the membrane are neutral, facilitating pass-through of the contaminant. If, for instance, a contaminant is negatively charged at neutral pH, it is often desirable to lower the pH of the feed solution to protonate the contaminant. For example, removal of phosphate is facilitated by lowering the pH of the solution to about 3, which protonates the phosphate anion, allowing passage through a membrane. As shown in Example 5, a decrease in pH from 7.5 to 3.0 decreases the percentage of GlcNAc passing through a polyamide membrane such as an Osmonics MX07 in thirty minutes from 70% to 28%, while increasing the pass percentage of phosphate from 10% to 46% (see, Example 6, Table 5 for additional examples of the effect of pH change on passage rate of other compounds through various nanofiltration membranes). For purification of an anionic carbohydrate, the pH will generally between about pH 1 and about pH 7. Conversely, if contaminant has a positive surface charge, the pH of the feed solution can be adjusted to between about pH 7 and about pH 14. For example, increasing the pH of a solution containing a contaminant having an amino group (xe2x80x94NH3+) will make the amino group neutral, thus facilitating its passage through the membrane. Thus, one aspect of the invention involves modulating a separation by adjusting the pH of a solution in contact with the membrane; this can change the ionic charge of a contaminant and can also affect the surface charge of the membrane, thus facilitating purification if the desired carbohydrate. Of course, the manufacturer""s instructions must be followed as to acceptable pH range for a particular membrane to avoid damage to the membrane.
For some applications, a mixture is first subjected to nanofiltration or reverse osmosis at one pH, after which the retentate containing the saccharide of interest is adjusted to a different pH and subjected to an additional round of membrane purification. For example, filtration of a reaction mixture used to synthesize sialyl lactose through an Osmonics MX07 membrane (a nanofiltration membrane having a MWCO of about 500 Da) at pH 3.0 will retain the sialyl lactose and remove most phosphate, pyruvate, salt and manganese from the solution, while also removing some of the GlcNAc, lactose, and sialic acid. Further recirculation through the MX07 membrane after adjusting the pH of the retentate to 7.4 will remove most of the remaining phosphate, all of the pyruvate, all of the lactose, some of the sialic acid, and substantial amounts of the remaining manganese.
If a saccharide is to be purified from a mixture that contains proteins, such as enzymes used to synthesize a desired oligosaccharide or nucleotide sugar, it is often desirable to remove the proteins as a first step of the purification procedure. For a saccharide that is smaller than the proteins, this separation is accomplished by choosing a membrane that has an MWCO which is less than the molecular mass of the protein or other macromolecule to be removed from the solution, but is greater than the molecular mass of the oligosaccharide being purified (i.e., the rejection ratio in this case is higher for the protein than for the desired saccharide). Proteins and other macromolecules that have a molecular mass greater than the MWCO will thus be rejected by the membrane, while the saccharide will pass through the membrane. Conversely, if an oligosaccharide or nucleotide sugar is to be purified from proteins that are smaller than the oligosaccharide or nucleotide sugar, a membrane is used that has a MWCO that is larger than the molecular mass of the protein but smaller than that of the oligosaccharide or nucleotide sugar. Generally, separation of proteins from carbohydrates will employ membranes that are commonly referred to as ultrafiltration (UF) membranes. UF membranes that are suitable for use in the methods of the invention are available from several commercial manufacturers, including Millipore Corp. (Bedford, Mass.), Osmonics, Inc. (Minnetonka, Minn.), Filmtec (Minneapolis, Minn., UOP, Desalination Systems, Advanced Membrane Technologies, and Nitto.
The invention also provides methods for removing salts and other low molecular weight components from a mixture containing a saccharide of interest by using a nanofiltration (NF) or a reverse osmosis (RO) membrane. Nanofiltration membranes are a class of membranes for which separation is based both on molecular weight and ionic charge. These membranes typically fall between reverse osmosis and ultrafiltration membranes in terms of the size of species that will pass through the membrane. Nanofiltration membranes typically have micropores or openings between chains in a swollen polymer network. Molecular weight cut-offs for non-ionized molecules are typically in the range from 100-20,000 Daltons. For ions of the same molecular weight, membrane rejections (retentions) will increase progressively for ionic charges of 0, 1, 2, 3 etc. for a particular membrane because of increasing charge density (see, e.g., Eriksson, P., xe2x80x9cNanofiltration Extends the Range of Membrane Filtration,xe2x80x9d Environmental Progress, 7: 58-59 (1988)). Nanofiltration is also described in Chemical Engineering Progress, pp. 68-74 (March 1994), Rautenbach et al., Desalination 77:73 (1990), and U.S. Pat. No. 4,806,244). In a typical application, saccharides of interest will be retained by the nanofiltration membrane and contaminating salts and other undesired components will pass through. A nanofiltration membrane useful in the methods of the invention will typically have a retention characteristic for the saccharide of interest of from about 40% to about 100%, preferably from about 70% to about 100%. The nanofilter membranes used in the invention can be any one of the conventional nanofilter membranes, with polyamide membranes being particularly suitable. Several commercial manufacturers, including Millipore Corp. (Bedford, Mass.), Osmonics, Inc. (Minnetonka, Minn.), Filmtec, UOP, Advanced Membrane Technologies, Desalination Systems, and Nitto, among others, distribute nanofiltration membranes that are suitable for use in the methods of the invention. For example, suitable membranes include the Osmonics MX07, YK, GH (G-10), GE (G-5), and HL membranes, among others.
Reverse osmosis (RO) membranes also allow a variety of aqueous solutes to pass through them while retaining selected molecules. Generally, osmosis refers to a process whereby a pure liquid (usually water) passes through a semipermeable membrane into a solution (usually sugar or salt and water) to dilute the solution and achieve osmotic equilibrium between the two liquids. In contrast, reverse osmosis is a pressure driven membrane process wherein the application of external pressure to the membrane system results in a reverse flux with the water molecules passing from a saline or sugar solution compartment into the pure water compartment of the membrane system. A RO membrane, which is semipermeable and non-porous, requires an aqueous feed to be pumped to it at a pressure above the osmotic pressure of the substances dissolved in the water. An RO membrane can effectively remove low molecular weight molecules ( less than 200 Daltons) and also ions from water. Preferably, the reverse osmosis membrane will have a retention characteristic for the saccharide of interest of from about 40% to about 100%, preferably from about 70% to about 100%. Suitable RO membranes include, but are not limited to, the Filmtec BW-30, Filmtec SW-30, Filmtec SW-30HR, UOP RO membranes, Desal RO membranes, Osmonics RO membranes, Advanced Membrane Technologies RO membranes, and the Nitto RO membranes, among others. One example of a suitable RO membrane is Millipore Cat. No. CDRN500 60 (Millipore Corp., Bedford, Mass.).
The membranes used in the invention may be employed in any of the known membrane constructions. For example, the membranes can be flat, plate and frame, tubular, spiral wound, hollow fiber, and the like. In a preferred embodiment, the membrane is spiral wound. The membranes can be employed in any suitable configuration, including either a cross-flow or a depth configuration. In xe2x80x9ccross-flowxe2x80x9d filtration, which is preferred for ultrafiltration, nanofiltration and reverse osmosis purifications according to the invention,he xe2x80x9cfeedxe2x80x9d or solution from which the carbohydrate of interest is to be purified flows through membrane channels, either parallel or tangential to the membrane surface, and is separated into a retentate (also called recycle or concentrate) stream and a permeate stream. To maintain an efficient membrane, the feed stream should flow, at a sufficiently high velocity, parallel to the membrane surface to create shear forces and/or turbulence to sweep away accumulating particles rejected by the membrane. Cross-flow filtration thus entails the flow of three streamsxe2x80x94feed, permeate and retentate. In contrast, a xe2x80x9cdead endxe2x80x9d or xe2x80x9cdepthxe2x80x9d filter has only two streamsxe2x80x94feed and filtrate (or permeate). The recycle or retentate stream, which retains all the particles and large molecules rejected by the membrane, can be entirely recycled to the membrane module in which the recycle stream is generated, or can be partially removed from the system. When the methods of the invention are used to purify saccharides from lower molecular weight components, for example, the desired saccharides are contained in the retentate stream (or feed stream, for a depth filter), while the permeate stream contains the removed contaminants.
The purification methods of the invention can be further optimized by adjusting the pressure, flow rate, and temperature at which the filtration is carried out. UF, NF, and RO generally require increasing pressures above ambient to overcome the osmotic pressure of the solution being passed through the membrane. The membrane manufacturers"" instructions as to maximum and recommended operating pressures can be followed, with further optimization possible by making incremental adjustments. For example, the recommended pressure for UF will generally be between about 25 and about 100 psi, for NF between about 50 psi and about 1500 psi, and for RO between about 100 and about 1500 psi. Flow rates of both the concentrate (feed solution) and the permeate can also be adjusted to optimize the desired purification. Again, the manufacturers"" recommendations for a particular membrane serve as a starting point from which to begin the optimization process by making incremental adjustments. Typical flow rates for the concentrate (Pc) will be between about 1 and about 15 gallons per minute (GPM), and more preferably between about 3 and about 7 GPM. For the permeate, flow rates (Pf) of between about 0.05 GPM and about 10 GPM are typical, with flow rates between about 0.2 and about 1 GPM being preferred. The temperature at which the purification is carried out can also influence the efficiency and speed of the purification. Temperatures of between about 0 and about 100xc2x0 C. are typical, with temperatures between about 20 and 40xc2x0 C. being preferred for most applications. Higher temperatures can, for some membranes, result in an increase in membrane pore size, thus providing an additional parameter that one can adjust to optimize a purification.
In a preferred embodiment, the filtration is performed in a membrane purification machine which provides a means for automating control of flow rate, pressure, temperature, and other parameters that can affect purification. For example, the Osmonics 213T membrane purification machine is suitable for use in the methods of the invention, as are machines manufactured by other companies listed above.
The membranes can be readily cleaned either after use or after the permeability of the membrane diminishes. Cleaning can be effected at a slightly elevated temperature if so desired, by rinsing with water or a caustic solution. If the streams contain small amounts of enzyme, rinsing in the presence of small amounts of surfactant, for instance ULTRASIL(copyright), might be useful. Also, one can use prefilters (100-200 xcexcm) to protect the more expensive nanofiltration membranes. Other cleaning agents can, if desired, be used. The choice of cleaning method will depend on the membrane being cleaned, and the membrane manufacturer""s instructions should be consulted. The cleaning can be accomplished with a forward flushing or a backward flushing.
The purification methods of the invention can be used alone or in combination with other methods for purifying carbohydrates. For example, an ion exchange resin can be used to remove particular ions from a mixture containing a saccharide of interest, either before or after nanofiltration/reverse osmosis, or both before and after filtration. Ion exchange is particularly desirable if it is desired to remove ions such as phosphate and nucleotides that remain after a first round of nanofiltration or reverse osmosis. In the case of sialyl lactose synthesis as discussed above, this can be accomplished, for example, by adding an anion exchange resin such as AG1X-8 (acetate form, BioRad; see, e.g., BioRad catalog for other ion exchange resins) to a retentate that is at about pH 3.0 or lower until the phosphate concentration is reduced as desired. In this process, acetic acid is released, so one may wish to follow the ion exchange with an additional purification through the nanofiltration or reverse osmosis system. For example, one can circulate the pH 3.0 or lower solution through an Osmonics MX07 or similar membrane until the conductivity of the permeate is low and stabilized. The pH of the solution can then be raised to 7.4 with NaOH and the solution recirculated through the same membrane to remove remaining sodium acetate and salt. Cations can be removed in a similar manner; for example, to remove Mn2+, an acidic ion exchange resin can be used, such as AG50WX8 (H+) (BioRad).
The purification methods of the invention are particularly useful for purifying oligosaccharides that have been prepared using enzymatic synthesis. Enzymatic synthesis using glycosyltransferases provides a powerful method for preparing oligosaccharides; for some applications it is desirable to purify the oligosaccharide from the enzymes and other reactants in the enzymatic synthesis reaction mixture. Preferred methods for producing many oligosaccharides involve glycosyl transferase cycles, which produce at least one mole of inorganic pyrophosphate for each mole of product formed and are typically carried out in the presence of a divalent metal ion. Examples of glycosyltransferase cycles are the sialyltransferase cycles, which use one or more enzymes as well as other reactants. See, e.g., U.S. Pat. No. 5,374,541 WO 9425615 A, PCT/US96/04790, and PCT/US96/04824. For example, a reaction used for synthesis of sialylated oligosaccharides can contain a sialyltransferase, a CMP-sialic acid synthetase, a sialic acid, an acceptor for the sialyltransferase, CTP, and a soluble divalent metal cation. An exemplary xcex1(2,3)sialyltransferase referred to as xcex1(2,3)sialtransferase (EC 2.4.99.6) transfers sialic acid to the non-reducing terminal Gal of a Galxcex21xe2x86x923Glc disaccharide or glycoside. See, Van den Eijnden et al., J. Biol. Chem., 256;3159 (1981), Weinstein et al., J. Biol. Chem., 257:13845 (1982) and Wen et al, J. Biol. Chem., 267:21011 (1992). Another exemplary xcex12,3-sialyltransferase (EC 2.4.99.4) transfers sialic acid to the non-reducing terminal Gal of the disaccharide or glycoside. See, Rearick et al., J. Biol. Chem., 254:4444 (1979) and Gillespie et al., J. Biol. Chem., 267:21004 (1992). Further exemplary enzymes include Gal-xcex2-1 4-GlcNAcxcex1-2,6 sialyltransferase (See, Kurosawa et al. Eur. J. Biochem. 219:375-381 (1994)). The reaction mixture will also contain an acceptor for the sialyltransferase, preferably having a galactosyl unit. Suitable acceptors, include, for example, Galxcex21xe2x86x923GalNAc, lacto-N-tetraose, Galxcex21xe2x86x923GlcNAc, Galxcex21xe2x86x923Ara, Galxcex21xe2x86x926GlcNAc, Galxcex21xe2x86x924Glc (lactose), Galxcex21xe2x86x924Glcxcex21-OCH2CH3, Galxcex21xe2x86x924Glcxcex21-OCH2CH2CH3, Galxcex21xe2x86x924Glcxcex21-OCH2C6H5, Galxcex21xe2x86x924GlcNAc, Galxcex21-OCH3, melibiose, raffinose, stachyose, and lacto-N-neotetraose (LNnT). The sialic acid present in the reaction mixture can include not only sialic acid itself (5-N-acetylneuraminic acid; 5-N-acetylamino-3,5-dideoxy-D-glycero-D-galacto-2-nonulosonic acid; NeuAc, and sometimes also abbreviated AcNeu or NANA), but also 9-substituted sialic acids such as a 9-O-C1-C6 acyl-NeuAc like 9-O-lactyl-NeuAc or 9-O-acetyl-NeuAc, 9-deoxy-9-fluoro-NeuAc and 9-azido-9-deoxy-NeuAc. The synthesis and use of these compounds in a sialylation procedure is described in international application WO 92/16640, published Oct. 1, 1992.
In preferred embodiments the reaction medium can further comprise a CMP-sialic acid recycling system comprising at least 2 moles of phosphate donor per each mole of sialic acid, and catalytic amounts of an adenine nucleotide, a kinase capable of transferring phosphate from the phosphate donor to nucleoside diphosphates, and a nucleoside monophosphate kinase capable of transferring the terminal phosphate from a nucleoside triphosphate to CMP. For example, a suitable CMP-sialic acid regenerating system comprises cytidine monophosphate (CMP), a nucleoside triphosphate (for example adenosine triphosphate (ATP), a phosphate donor (for example, phosphoenolpyruvate or acetyl phosphate), a kinase (for example, pyruvate kinase or acetate kinase) capable of transferring phosphate from the phosphate donor to nucleoside diphosphates and a nucleoside monophosphate kinase (for example, myokinase) capable of transferring the terminal phosphate from a nucleoside triphosphate to CMP. The previously discussed xcex1(2,3)sialyltransferase and CMP-sialic acid synthetase can also be formally viewed as part of the CMP-sialic acid regenerating system. For those embodiments in which a CMP-sialic acid recycling system is not used, the reaction medium will preferably further comprise a phosphatase.
Pyruvate is a byproduct of the sialyltransferase cycle and can be made use of in another reaction in which N-acetylmannosamine (ManNAc) and pyruvate are reacted in the presence of NeuAc aldolase (EC 4.1.3.3) to form sialic acid. Alternatively, advantage can be taken of the isomerization of GlcNAc to ManNAc, and the less expensive GlcNAc can be used as the starting material for sialic acid generation. Thus, the sialic acid can be replaced by ManNAc (or GlcNAc) and a catalytic amount of NeuAc aldolase. Although NeuAc aldolase also catalyzes the reverse reaction (NeuAc to ManNAc and pyruvate), the produced NeuAc is irreversibly incorporated into the reaction cycle via CMP-NeuAc catalyzed by CMP-sialic acid synthetase. In addition, the starting material, ManNAc, can also be made by the chemical conversion of GlcNAc using methods known in the art (see, e.g., Simon et al., J. Am. Chem. Soc. 110:7159 (1988). The enzymatic synthesis of sialic acid and its 9-substituted derivatives and the use of a resulting sialic acid in a different sialylating reaction scheme is disclosed in International application WO 92/16640, published on Oct. 1, 1992, and incorporated herein by reference.
When a galactosyltransferase is used for enzymatic synthesis of an oligosaccharide, the reaction medium will preferably contain, in addition to a galactosyltransferase, donor substrate, acceptor sugar and divalent metal cation, a donor substrate recycling system comprising at least 1 mole of glucose-1-phosphate per each mole of acceptor sugar, a phosphate donor, a kinase capable of transferring phosphate from the phosphate donor to nucleoside diphosphates, and a pyrophosphorylase capable of forming UDP-glucose from UTP and glucose-1-phosphate and catalytic amounts of UDP and a UDP-galactose-4-epimerase. Exemplary galactosyltransferases include xcex1(1,3) galactosyltransferase (E.C. No. 2.4.1.151, see, e.g., Dabkowski et al., Transplant Proc. 25: 2921 (1993) and Yamamoto et al., Nature 345:229-233 (1990)) and xcex2(1,4) galactosyltransferase (E.C. No. 2.4.1.38).
Oligosaccharides synthesized by other enzymatic methods can also be purified by the methods of the invention. For example, the methods are useful for purifying oligosaccharides produced in non-cyclic or partially cyclic reactions such as simple incubation of an activated saccharide and an appropriate acceptor molecule with a glycosyltransferase under conditions effective to transfer and covalently bond the saccharide to the acceptor molecule. Glycosyltransferases, which include those described in, e.g., U.S. Pat. No. 5,180,674, and International Patent Publication Nos. WO 93/13198 and WO 95/02683, as well the glycosyltransferases encoded by the los locus of Neisseria (see, U.S. Pat. No. 5,545,553), can be bound to a cell surface or unbound. Oligosaccharides that can be obtained using these glycosyltransferases include, for example, Galxcex1(1xe2x86x924)Galxcex2(1xe2x86x924)Glc, GlcNAcxcex2(1,3)Galxcex2(1,4)Glc, Galxcex2(1xe2x86x924)GlcNAcxcex2(1xe2x86x923)Galxcex2(1xe2x86x924)Glc, and GalNAcxcex2(1xe2x86x923)Galxcex2(1xe2x86x924)GlcNAcxcex2(1xe2x86x923)Galxcex2(1xe2x86x924)Glc, among many others.
Among the compounds that one can purify using the described methods are sialic acid and any sugar having a sialic acid moiety. These include the sialyl galactosides, including the sialyl lactosides, as well as compounds having the formula:
NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924)GlcN(Rxe2x80x2)xcex2xe2x80x94OR
or
NeuAcxcex1(2xe2x86x923)Galxcex2(1xe2x86x924)GlcN(Rxe2x80x2)xcex2(1xe2x86x923)Galxcex2xe2x80x94OR
In these formulae, Rxe2x80x2 is alkyl or acyl from 1-18 carbons, 5,6,7,8-tetrahydro-2-naphthamido; benzamido; 2-naphthamido; 4-aminobenzamido; or 4-nitrobenzamido. R is a hydrogen, a alkyl C1-C6, a saccharide, an oligosaccharide or an aglycon group having at least one carbon atom. The term xe2x80x9caglycon group having at least one carbon atomxe2x80x9d refers to a group xe2x80x94Axe2x80x94Z, in which A represents an alkylene group of from 1 to 18 carbon atoms optionally substituted with halogen, thiol, hydroxy, oxygen, sulfur, amino, imino, or alkoxy; and Z is hydrogen, xe2x80x94OH, xe2x80x94SH, xe2x80x94NH2, xe2x80x94NHR1, xe2x80x94N(R1)2, xe2x80x94CO2H, xe2x80x94CO2R1, xe2x80x94CONH2, xe2x80x94CONHR1, xe2x80x94CON(R1)2, xe2x80x94CONHNH2, or xe2x80x94OR1 wherein each R1 is independently alkyl of from 1 to 5 carbon atoms. In addition, R can be 
where n,m,o=1-18; (CH2)n-R2 (in which n=0-18), wherein R2 is a variously substituted aromatic ring, preferably, a phenyl group, being substituted with one or more alkoxy groups, preferably methoxy or O(CH2)mCH3, (in which m=0-18), or a combination thereof. R can also be 3-(3,4,5-trimethoxyphenyl)propyl.
The present invention is also useful for purifying a variety of compounds that comprise selectin-binding carbohydrate moieties. These selectin-binding moieties have the general formula:
R1Galxcex21,m(Fucxcex11,n)GlcNR0(R2)pxe2x80x94
in which R0 is (C1-C8 alkyl)carbonyl, (C1-C8 alkoxy)carbonyl, or (C2-C9 alkenyloxy)carbonyl, R1 is an oligosaccharide or a group having the formula 
R3 and R4 may be the same or different and may be H, C1-C8 alkyl, hydroxy-(C1-C8 alkyl), aryl-(C1-C8 alkyl), or (C1-C8 alkoxy)-(C1-C8 alkyl), substituted or unsubstituted. R2 may be H, C1-C8 alkyl, hydroxy-(C1-C8 alkyl), aryl-(C1-C8 alkyl), (C1-C8 alkyl)-aryl, alkylthio, xcex11,2Man, xcex11,6GalNAc, xcex21,3Galxcex21,4Glc, xcex11,2Man-R8, xcex11,6GalNAc-R8, and xcex21,3Gal-R8. R8 may be H, C1-C8 alkyl, C1-C8 alkoxy, hydroxy-(C1-C8 alkyl), aryl-(C1-C8 alkyl), (C1-C8 alkyl)-aryl, or alkylthio. In the formula, m and n are integers and may be either 3 or 4; p may be zero or 1.
The substituted groups mentioned above may be substituted by hydroxy, hydroxy(C1-C4 alkyl), polyhydroxy(C1-C4 alkyl), alkanoamido, or hydroxyalknoamido substituents. Preferred substituents include hydroxy, polyhydroxy(C3 alkyl), acetamido and hydroxyacetamido. A substituted radical may have more than one substitution, which may be the same or different.
For embodiments in which R1 is an oligosaccharide, the oligosaccharide is preferably a trisaccharide. Preferred trisaccharides include NeuAcxcex12,3Galxcex21,4GlcNAcxcex21,3 or NeuGcxcex12,3Galxcex21,4GlcNAcxcex21,3.
For embodiments in which R1 is the group having the formula 
R3 and R4 preferably form a single radical having the formula
xe2x80x94R5xe2x80x94or xe2x80x94(R6)qxe2x80x94Oxe2x80x94(R7)rxe2x80x94
in which R5 is C3-C7 divalent alkyl, substituted or unsubstituted, R6 and R7 are the same or different and are C1-C6 divalent alkyl, substituted or unsubstituted. In the formula, q and r are integers which may be the same or different and are either zero or 1. The sum of q and r is always at least 1.
A more preferred structure for a single radical formed by R3 and R4 is one having the formula
xe2x80x94(R6)xe2x80x94Oxe2x80x94
in which R6 is C3-C4 divalent alkyl, substituted or unsubstituted. For instance, R6 may have the formula xe2x80x94CH2xe2x80x94CH2xe2x80x94CH2xe2x80x94CH2xe2x80x94, preferably substituted. The radical can be substituted with hydroxy, polyhydroxy(C3 alkyl), and substituted or unsubstituted alkanoamido groups, such as acetamido or hydroxyacetamido. The substituted structure will typically form a monosaccharide, preferably a sialic acid such as NeuAc or NeuGc linked xcex12,3 to the Gal residue.
In the general formula, above, both m and n are integers and can be either 3 or 4. Thus, in one set of structures Gal is linked xcex21,4 and Fuc is linked xcex11,3 to GlcNAc. This formula includes the SLex tetrasaccharide. SLex has the formula NeuAcxcex12,3Galxcex21,4(Fucxcex11,3)GlcNAcxcex21xe2x80x94. This structure is selectively recognized by LECCAM-bearing cells. SLex compounds that can be purified using the methods of the invention include NeuAcxcex12,3Galxcex21,4(Fucxcex11,3)GlcNAcxcex21-Gal-OEt, NeuAcxcex11,3Galxcex21,4(Fucxcex11,3)GlcNAcxcex21,4Galxcex21-OEt, and others that are described in international application WO 91/19502. Other compounds that one can purify using the methods include those described in U.S. Pat. No. 5,604,207 having the formula 
wherein Z is hydrogen, C1-C6 acyl or 
Y is selected from the group consisting of C(O), SO2, HNC(O), OC(O) and SC(O);
R1 is selected from the group consisting of an aryl, a substituted aryl and a phenyl C1-C3 alkylene group, wherein said aryl substituent is selected from the group consisting of a halo, trifuloromethyl, nitro, C1-C18 alkyl, C1-C18 alkoxy, amino, mono-C1-C18 alkylamino, di-C1-C18 alkylamino, benzylamino, C1-C18 alkylbenzylamino, C1-C18 thioaklyl and C1-C18 alkyl carboxamido groups, or
R1Y is allyloxycarbonyl or chloroacetyl;
R2 is selected from the group consisting of monosaccharide (including xcex21,3Gal-OR, where R=H, alkyl, aryl or acyl), disaccharide, hydrogen, C1-C18 straight chain, branched chain or cyclic hydrocarbyl, C1-C6 alkyl, 3-(3,4,5-trimethoxyphenyl)propyl, C1-C5 alkylene xcfx89-carboxylate, xcfx89-trisubstituted silyl C2-C4 alkylene wherein said xcfx89-trisubstituted silyl is a silyl group having three substituents independently selected from the group consisting of C1-C4 alkyl, phenyl,
or OR2 together form a C1-C18 straight chain, branched chain or cyclic hydrocarbyl carbamate;
R3 is hydrogen or C1-C6 acyl;
R4 is hydrogen, C1-C6 alkyl or benzyl;
R5 is selected from the group consisting of hydrogen, benzyl, methoxybenzyl, dimethoxybenzyl and C1-C6 acyl;
R7 is methyl or hydroxymethyl; and
X is selected from the group consisting of C1-C6 acyloxy, C2-C6 hydroxylacyloxy, hydroxy, halo and azido.
A related set of structures included in the general formula are those in which Gal is linked xcex21,3 and Fuc is linked xcex11,4. For instance, the tetrasaccharide, NeuAcxcex12,3Galxcex21,3(Fucxcex11,4)GlcNAcxcex21xe2x80x94, termed here SLea, is recognized by selectin receptors. See, Berg et al., J. Biol. Chem., 266:14869-14872 (1991). In particular, Berg et al. showed that cells transformed with E-selectin cDNA selectively bound neoglycoproteins comprising SLea.
The methods of the invention are also useful for purifying oligosaccharide compounds having the general formula Galxcex11,3Galxe2x80x94, including Galxcex11,3Galxcex21,4Glc(R)xcex2xe2x80x94Oxe2x80x94R1, wherein R1 is xe2x80x94(CH2)nxe2x80x94COX, with X=OH, OR2, xe2x80x94NHNH2, R=OH or NAc, and R2 is a hydrogen, a saccharide, an oligosaccharide or an aglycon group having at least one carbon atom, and n=an integer from 2 to 18, more preferably from 2 to 10. For example, one can purify a compound having the formula Galxcex11,3Galxcex21,4GlcNAcxcex2xe2x80x94Oxe2x80x94(CH2)5xe2x80x94COOH using procedures such as those described in Examples 7-8. Also among the compounds that can be purified according to the invention are lacto-N-neotetraose (LNnT), GlcNAcxcex21,3Galxcex21,4Glc (LNT-2), sialyl(xcex12,3)-lactose, and sialyl(xcex12,6)-lactose.
In the above descriptions, the terms are generally used according to their standard meanings. The term xe2x80x9calkylxe2x80x9d as used herein means a branched or unbranched, saturated or unsaturated, monovalent or divalent, hydrocarbon radical having from 1 to 20 carbons, including lower alkyls of 1-8 carbons such as methyl, ethyl, n-propyl, butyl, n-hexyl, and the like, cycloalkyls (3-7 carbons), cycloalkylmethyls (4-8 carbons), and arylalkyls. The term xe2x80x9calkoxyxe2x80x9d refers to alkyl radicals attached to the remainder of the molecule by an oxygen, e.g., ethoxy, methoxy, or n-propoxy. The term xe2x80x9calkylthioxe2x80x9d refers to alkyl radicals attached to the remainder of the molecule by a sulfur. The term of xe2x80x9cacylxe2x80x9d refers to a radical derived from an organic acid by the removal of the hydroxyl group. Examples include acetyl, propionyl, oleoyl, myristoyl.
The term xe2x80x9carylxe2x80x9d refers to a radical derived from an aromatic hydrocarbon by the removal of one atom, e.g., phenyl from benzene. The aromatic hydrocarbon may have more than one unsaturated carbon ring, e.g., naphthyl.
The term xe2x80x9calkoxyxe2x80x9d refers to alkyl radicals attached to the remainder of the molecule by an oxygen, e.g. ethoxy, methoxy, or n-propoxy.
The term xe2x80x9calkylthioxe2x80x9d refers to alkyl radicals attached to the remainder of the molecule by a sulfur.
An xe2x80x9calkanoamidoxe2x80x9d radical has the general formula xe2x80x94NHxe2x80x94COxe2x80x94(C1-C6 alkyl) and may or may not be substituted. If substituted, the substituent is typically hydroxyl. The term specifically includes two preferred structures, acetamido, xe2x80x94NHxe2x80x94COxe2x80x94CH3, and hydroxyacetamido, xe2x80x94NHxe2x80x94COxe2x80x94CH2xe2x80x94OH.
The term xe2x80x9cheterocyclic compoundsxe2x80x9d refers to ring compounds having three or more atoms in which at least one of the atoms is other than carbon (e.g., N, O, S, Se, P, or As). Examples of such compounds include furans (including the furanose form of pentoses, such as fucose), pyrans (including the pyranose form of hexoses, such as glucose and galactose) pyrimidines, purines, pyrazines and the like.
The methods of the invention are useful not only for purifying carbohydrates that that are newly synthesized, but also those that are the products of degradation, e.g., enzymatic degradation. See, e.g., Sinnott, M. L., Chem. Rev. 90: 1171-1202 (1990) for examples of enzymes that catalyze degradation of oligosaccharides.
The invention also provides methods for purifying nucleotides, nucleotide sugars, and related compounds. For example, a nucleotide sugar such as GDP-fucose, GDP-mannose, CMP-NeuAc, UDP-glucose, UDP-galactose, UDP-N-acetylgalactosamine, and the like, can be purified by the methods described herein. The methods are also useful for purifying nucleotides and nucleotides in various states of phosphorylation (e.g., CMP, CDP, CTP, GMP, GDP, GTP, TMP, TDP, TTP, AMP, ADP, ATP, UMP, UDP, UTP), as well as the deoxy forms of these and other nucleotides.
The following examples are offered solely for the purposes of illustration, and are intended neither to limit nor to define the invention.